Save as Image, without white space

Hello,

I'm using MarvinSketch 5.3.8 (MacOSX). In the File menu, I can select Save As Image, but it saves the entire sketch space (i.e., my structure plus the surrounding white space). It there a way to automatically save just the structure?

Thanks!

Porscha

The "File/Save As Image" action creates a snapshot about your canvas. If you need only the relevant part of the canvas, save the drawn structure as MRV then convert it to image with the help of the MolConverter tool.

/Applications/ChemAxon/MarvinBeans/bin/molconvert png:w400,h400 drawnstructure.mrv -o drawnstructure.png

You can read more about MolConverter in the user manual: Molecule File Conversion with MolConverter.

When you save compound with Save As Image option in sketcher, I recommend to fit the structure to the canvas size (choose "All" scale option) to decrease the empty space around the structure.

Hello,
Thanks.

A few more questions:
1. If I download a
SDF from pubchem, I have two options to save called  "2D SDF:Save" or
"3D SDF:Save". If I drag either of these files into MarvinSketch, I get
the structures shown in the attached screenshot.  Is there a way to
display them as wedge-type structures, such as those shown on the left
here:
http://courses.chem.psu.edu/chem210/tutorials/stereo-drawings/stereo-tutorial.html />
2. I tried to open a terminal and type the following as suggested:
/Applications/ChemAxon/MarvinBeans/bin/molconvert png:w400,h400 drawnstructure.mrv -o drawnstructure.png
but I get output
"drawnstructure.mrv: not found"
(the path is correct, I installed MarvinSketch in my Applications folder)
What am I doing wrong? Is there an additional plugin or download I  need?

Thanks!
Porscha

> To: po_louise _at_ hotmail.com
>
Subject: Topic Reply Notification - Save as Image, without white space
< Drawing & visualization: Marvin/Sketch /View /Space <
Support
> From: forum _at_ chemaxon.com
> Date: Wed, 6 Oct 2010 15:01:02 +0200
>
>
> Hello Porscha McRobbie,
>
>
You are receiving this email because you are watching the topic, 'Save
as Image, without white space' at Technical Support Forum.
>
> Subject:
> Author: Tamas
>
The "File/Save As Image" action creates a snapshot about your canvas.
If you need only the relevant part of the canvas, save the drawn
structure as MRV then convert it to image with the help of the
MolConverter tool.
> /Applications/ChemAxon/MarvinBeans/bin/molconvert png:w400,h400 drawnstructure.mrv -o drawnstructure.png
> You can read more about MolConverter in the user manual: Molecule File Conversion with MolConverter.
>
When you save compound with Save As Image option in sketcher, I
recommend to fit the structure to the canvas size (choose "All" scale
option) to decrease the empty space around the structure....
>
> Click here to visit the topic: http://www.chemaxon.com/forum/viewtopic.php?p=31267#31267 />>
> If you no longer wish to watch this topic click the "Stop watching this topic link" found at the topic page.
>
> --
> ChemAxon Technical Support Forums

Hi Porscha,

 

1. The wedge bonds should be defined in your SDFile, otherwise Marvin will not display it.

2. "drawnstructure.mrv" means the file you have drawn and saved.

 

Best regards,

 

Akos

Just one more note. If you like to quote a previous post, I recommend the usage of the "Quote" button in the top-right corner of the box of the desired post. I believe it is more easier than pasting some text from the forum notification mail. Of course, it is only an advice. You can choose how to quote something.

akospapp wrote:

Hi Porscha,   1. The wedge bonds should be defined in your SDFile, otherwise Marvin will not display it. 2. "drawnstructure.mrv" means the file you have drawn and saved.   Best regards,   Akos

Hi,

I'm looking at the structure for tetramethrin from pubchem, and have a question about the structure checker.

1. In general, should I download the 3D SDF instead of the 2D SDF? Both give wedge bonds....

(structures on the left are 2D, those on the right are 3D in what follows)

2. After I drag into MarvinSketch, I get "Problems: 1" at the bottom.  A single click fixes it for the 2D SDF file (left), but does not with the 3D SDF (right). For the 3D file, I can click "Fix All" many times and the "Problem" does not go away. Any advice?

3. In the future,  I want to import many structures in batch, and save each as an image. Will it be possible to automatically fix the problems (writing code?), without having to use the GUI and clicking for each structure?

Thanks,

Porscha

Hi,

 

The checkers are to warn you that there might be problems with your sketch; it is not sure that the automatic fixes will correct your structure.

In the next version, 5.4 (coming at the end of the month) there will be a Structure Checker version that can be used in batch mode, but it will require a separate license. This product will be able to filter your SDFile, and separate the correct structures from the structures with issues. For more information please see the Structure Checker presentation that was made on our US UGM in September:

 

https://www.chemaxon.com/wp-content/uploads/2010/07/StructureChecker.pdf

 

Best regards,

 

Akos